AMBER Archive (2002)

Subject: Re: Reorder water in amber7

From: Carlos Simmerling (carlos.simmerling_at_sunysb.edu)
Date: Tue Jun 11 2002 - 06:36:04 CDT

to turn off this feature (to track water) you
can make sure that the MACHINE file
does not have the -ROWAT flag.
Using this flag does improve code
efficiency and noticably helps scaling on
our Linux cluster. Look at the code
for details (look for ifdef ROWAT).
Carlos

----- Original Message -----
From: "Peter Varnai" <Peter.Varnai_at_ibpc.fr>
To: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Tuesday, June 11, 2002 4:38 AM
Subject: Reorder water in amber7

> Dear AMBER-group,
>
> "Reorder water Setup" appeared in the amber7 output
> files but I could not find documentation about it.
>
> What is the reason to do reordering of waters at each
> startup? This way I can't follow up the trajectory of a
> specific WAT in a concatenated trajectory? E.g. to see
> if the crystal waters have moved or not ...
>
> Thank you,
> Peter Varnai
>
>